Scars
by Ghost Fox Goddess
Summary: team Flash and metas are taken by Eiling and Eobard. Eiling wants to experiment on them for further research. Eobard wants the team to pay for what they did to him. Team Flash gets the worst of it: Barry is hurt the most and his friends are made to suffer by watching his pain. how will it turn out in the end? Will Barry be Barry again or will he Scar forever?- DISCONTINUED (sorry)
1. Chapter 1

**Barry Allen is a forensic scientist that works for the CCPD. Barry has a lab upstairs that he shares with Julian Albert, who as been alchemy but has never know it. Barry lives with Joe and Iris West, but recently Wally West moved in. Wally is Iris' brother and Joe's son, but because of alchemy he is a speedster. Barry has faced lots of threats like the reverse flash, zoom and captain cold, but now he faces a greater threat: savitar. Barry became the Flash after the particle accelerator failed which also created lots of metahumans like mirror master and blackout. Team Flash had stopped Caitlin who had turned into killer frost. recently The Flash and his allies (arrow, supergirl, white canary, atom, Firestorm and more) faced an alien race called the dominators who wanted to eliminate all metahumans including the flash in order the save their race. Everyone went back to where they are needed the most, which to Barry is Central City.**

 **My name is Barry Allen and I'm the fastest man alive. when I was a child I saw my mother killed by something impossible. my father went to prison for her murder. then an accident made me the impossible. to the outside world, I'm an ordinary forensic scientist, but secretly I use my speed to fight crime and find others like me. and one day, i'll find who killed my mother and get justice for my father. I am the flash.**

Barry walked to work instead of running at super speed like he usually did. He walked past Joe who was in the office talking to the police captain: David Singh. He walked upstairs tohis non stressful lab.

"Allen, finally, I was wondering when you were going to arrive" a voice said for behind him.

"Hi Julian" Barry said.

"For some one with super speed, you are always late" Julian said.

"I walked and I'm not late, I still have five minutes before I'm late" Barry replied.

"you walked?" Julain asked.

"I don't run everywhere you know" Barry replied.

"Barry? can I have a word?" Joe said from the door way.

"sure Joe" Barry replied.

"what is this?" Joe asked.

"that would be my notebook" Barry replied.

"i know its a notebook, but I'm talking about whats in it" Joe said.

"i don't know what you mean?" Barry asked confused.

"this" Joe said as he opened it.

"what is that?" Barry asked.

"that's what I'm asking you" Joe said.

"i don't know, I honestly don't know" Barry replied.

Joe had opened it to a page where there was pictures of Cisco Ramon, Caitlin Snow, Barry Allen, Wally West, Jefferson Jackson, Martin Stein, Jesse Quick and Kara Danvers. all of them had red circles around them like they were being targeted.

"to me that looks like someone is targeting you and the others on here" Joe said.

"Why?" Julian asked.

Barry took it off of Joe and carefully looked at it.

"i think I know why" Barry said.

"why?" Joe asked.

"we are all meta humans, except for kara who is an alien" Barry said.

"so we're taking about experiments?" Joe asked.

"Most likely" Barry said.

the conversation ended when Barry's phone started ringing. Barry speeded to his phone and saw it was Cisco.

"Hi Cisco" Barry answered the phone.

 _"I need you to come the S.T.A.R labs now"_ Cisco said over the phone.

"why?" Barry asked.

 _"i will explain when your here, I don't want to say it over the phone"_ Cisco replied.

"ok, ill be there in a minute" Barry hung up.

"Cisco wants me to come to S.T.A.R labs and he hasn't said why" Barry said.

"ok, ill tell Singh that you fell sick and have to get home right away and then ill meet you there" Joe said.

"Ok" Barry replied.

Barry took off in a Flash to S.T.A.R labs leaving Julian in the lab as Joe went to the captains office.

Barry was at S.T.A.R labs in no time. He expects a metahuman to be there but turns to see Cisco and Caitlin said at their usual desk like always.

"hi Barry" a female voice said behind him.

Barry turns around the see Oliver Queen and Felicity Smoak standing there behind him.

"what are you two doing here?" Barry asks.

"the Legends came earlier today to say that stein and Jax have been kidnapped" Oliver replied.

"the book, someone really is targeting us" Barry muttered to himself.

"What is it?" Felicity asked.

"just before Cisco called me, Joe came to talk to me, he showed me my notebook and there were pictures of me, Cisco, Caitlin, Wally, Jax, Stein, Jesse and Kara, red cirles around our picture. we found out someone is targeting us" Barry explained.

"Why just you guys?" Oliver said.

"because we are either a metahuman or an alien" Barry said.

Joe walked into the cortex. He saw Oliver and Felicity.

"Whats going on?" Joe asked.

"Jax and Stein have been kidnapped" Felicity replied.

"so the book-" Joe started.

"yeah, I believe we're next" Barry said.

"how do you know that?" Joe said.

"Because we are just here, Jesse and Kara are back on their earths, Jax and Stein are already gone so us four are the next targets" Barry replied.

Joe pulled out his phone and rang Wally.

 _"hi, whats wrong?"_ Wally asked.

"i need you to come to S.T.A.R labs now" Joe said.

 _"Should Iris come?"_ Wally asked.

"yeah" Joe hung up.

"is Wally coming then?" Cisco asked.

"yeah, and Iris" Joe replied.

"so what are we going to do?" Caitlin asked.

"we'll discuss it when Iris and Wally get here" Barry answered.

"we're here!" Wally called as he walked with Iris into the Cortex.

"why did you want us here?" Iris asked.

"me, Wally, Cisco, Caitlin, supergirl, jesse and firestorm are being targeted. firestorm has already been kidnapped and we are not sure about supergirl or jesse as they are back on their earths" Barry briefly explained.

"targeted by who?" Wally asked.

"we don't know" Barry replied.

Olivers phone vibrated in his pocket. he looked to see who it was from. Thea Queen had texted Oliver to tell him that he was need back at star city.

"We have to go, Thea needs me back at star city" Oliver explained.

"so we'll see you around then" Barry said.

"bye" felicity said as she and oliver walked out.

All of a sudden the lights flickered and there stood a man.


	2. Chapter 2

the lights flickered and there stood a man. the man walked out of the shadows and into the room. into the light.

the man stood in front of them is Eobard Thawne, the Reverse Flash.

"How are you still alive?" Joe asked angrily.

"that's none of your concern" Thawne replied.

"you dare show you face here for what you've done" Iris said angrily.

"i don't really care what I've done, everything I have done is for a good reason" Thawne replied emotionless.

"don't care?!" Iris said.

"not really, who ever ive killed or injured was someone not worth anything" Thawne said with a grin on his face.

"you killed lots of people" iris said.

"if you think that they're not worthless, name people that are worth something" Thawne said in a teasing way.

"ok. Eddie Thawn, Nora Allen, Harrison Wells, Mason Bridge and countless others" Iris said.

"who aren't even worth a penny" Eobard Thawne relied heartlessly.

"How are you still alive?" Joe asked again.

"if you really want to know" He replied "Flashpoint."

"flashpoint?" Cisco said.

"Yeah, when Barry saved his mother that night, I wasn't erased from existence" Eobard replied.

"so you can blame Barry for this" another voice said.

the turned to look behind Reverse Flash only to see General Eiling walking into the room.

"so you two are working together now?" Caitlin asked.

"sort of, but yes. he gets what he wants and I get what I want" Eobard said.

the room became a bit foggy as gas was released into the room.

"so your gassing us?" Wally said.

the gas stopped coming in and the room was clear again.

"was that supposed to do something?" Wally asked confused.

"it has" Eiling said.

reverse flash fired a glue like substance at all of them from a sort of like gun. the six of them were stuck to the walls. Barry tried to phase through it but his powers weren't working.

"anti-metahuman powers gas?" Barry asked.

"that's a way to put it, but yes. cant have you running out on us" Eiling replied.

"what is this stuff?" cisco asked.

"its just too hold you there while we get ready" Eiling said.

"if this holds us, then why the gas?" Wally asked.

"Caitlin and cisco's powers could get you out, but speed does nothing, it doesn't matter how fast you move, friction doesn't have an effect" Eiling replied.

"Time to take out the trash" Reverse Flash said as he knocked them out.

Julian was hidden inside a storage closet. he watched as the Reverse Flash and Eiling took team Flash. he didn't come out because he could take them out by him self. even if he tried, he would be taken too. he looks around the room to make sure they have completely gone. not a single noise was around except the calm breathing of his own breath.

Julian gets out of the storage closet and into the cortex. he saw Barry's phone on the side. he grabbed it and unlocked the phone, which was easy because there was no password. strange as you would have thought a superhero would have a password in case someone goes on it and looks at all of his stuff. he clicked on phone and went to find green arrow. he couldn't find green arrow or arrow. he remembered his face. the arrow is Oliver Queen, he had seen his on the news. he scrolled on the contacts until he found Oliver Queen. he clicked on his name and started ringing him.

 _"hi, Barry"_ Oliver said.

"I'm not Barry, I'm Julian Albert, I work with Barry as a forensic as well and I know hes the Flash. its complicated" Julian said.

 _"where's Barry"_ Oliver asked.

"He and the rest have been kidnapped by Reverse Flash and General Eiling" Julian replied.

 _"I'm coming"_ Oliver hung up.


	3. Chapter 3

they woke up to find themselves in a strange place which they thought is a military base. they were all in separate cells. they saw Jax, Stein, Jesse and Kara in cells as well. it was a circular room so everyone could see everyone. Jax and Stein were on opposite sides of the room so they couldn't become firestorm. Karas cell has kryptonite bars so she was weak. Caitlin had Anti-power cuffs on to stop her from using her power, so did cisco. the three speedsters had nothing stopping them from using their powers. the rest didn't need anything as they weren't a metahuman or an alien.

Eiling and Eobard came walking into the dismal room of imprisonment.

"glad to see your all awake" Eiling said.

a group of scientists came into the room with needles. they walked to Wally, Jesse and Barry's cells. they unlocked them and walked in. they grabbed their arms and injected them with something that stopped them from using their powers.

"you wouldn't be using your powers for a long time" Eobard said.

"why do you want us?" Jax asked.

"your know soon enough" Eobard said speeding to a chair near the door.

there was a table in the middle of the room and it had restraints on it. the cells didn't go all away around the room, they didn't cover near the door or opposite the door. opposite the door there was exposed wall with chairs near the top of the wall. the scientists walked out of the room and back again holding a metal dish, a scalpel which was a glowing green, chemicals and a lead box which looked important. they didn't want to know what that were for.

"Grab her" Eiling pointed to Kara.

a scientist with long black hair grabbed her out of her cell and threw her on the floor. she was strapped to the table, the red cape fell to the ground as it was tore off of the suit. the symbol of hope meant nothing to them as they took the scalpel and put it near her arm. Eiling and Thawne went out of the room.

everyone knew what was going to happen next: torture.

the scalpel was taken away from her arm, instead the scientist grabbed her sleeve and tore half of it off and throwing it on the dusty floor like a dirty rag. the scalpel cut across her kyriptonian arm drawing blood. kara instantly knew the scalpel was made from kryptonite. she was cut again and again and again. blood was pouring from her arm. the blood dripped onto the floor. Drip. Drip. Drip. the floor was stained red in that one area.

what were they accomplishing by doing this? Humour? Happiness? Joy? they were insane.

the scalpel was brought to her arm again. this time it wasnt deep like the rest of the cuts. a layer of skin was cut off and put onto the metal dish.

were they experimenting on her? testing her? seeing what her cells were like? is this what they want? to kill them all for their curiosity? she didn't want to know.

"have you got the skin sample?" a man from the doorway asked.

"yes" a cruel, emotionless answer.

the man walked in and grabbed the dish. he then walked out like he just brought a packet of sweets from a sweet shop instead of a skin sample from a cruel lab.

two more scientists came into the room. the first woman nodded and walked out. supergirl was unstrapped from the table and thrown into her cell. the cell was locked leaving a pained, bleeding girl in a cell with no treatment.

"Hey!" Barry shouted at the scientists.

"Barry, what are you doing?" Joe whispered to Barry from his cell which is next to Barry's.

"are you seriously going to leave her like that? she will die, you have cut through an artery, she will bleed to death and with the kryptonite she wont heal" Barry argued

the scientists rolled there eyes and walked out but to Barry's and everyones surprise, they came back with a bandage and first aid stuff. they locked the cell after they got in in case she tried to escape. they treated her wound she it wouldn't bleed out but left it painful. they got out and left the room, closing the door.

"thanks Barry" Kara said grateful that Barry had made them do that.

"no problem" Barry replied.

"there was a problem though Barry. what if they didn't help her, they could of done something bad to you for saying something like that" Joe said.

"But they didn't" Barry replied.

"that's not what I'm saying" Joe replied.

"they're going to do it to all or most of us anyway" Barry said.

everyone was sat in their cell leaning against a cold, uncomfortable wall. they sat in silence for five minutes before Caitlin decided to say something.

"Barry? how did you know they cut through an artery?" she asked.

"Lucky guess?" Barry replied.

Caitlin was going to reply to that obvious lie but three more scientists walked into the room. it was so quiet that you could be able to hear a pin drop. they looked around to try and find someone to take. Eiling wanted experiments and Thawn wanted revenge. the scientists knew who would fit into both plans.

They walked to Barry's cells, unlocked it and walked him to another room.

"where are you taking me?" Barry asked unsure why they were taking him to another room.

Barry was taken to a room which looked more like a nice lab: white, clean and had more tech and equipment. he was placed on a table and was chained to the table. a bigger scalpel was taken out by a mna with blonde hair while a woman with short blonde hair took his shirt off.

"what are you doing?" Barry asked.

"something that will hurt, so try not to move, the more you move the more painful it will be" she said.

the scalpel was given to the woman who cut across his abdomen. he clenched his jaw trying not to scream. he immediately started to bleed. she carefully and quickly removed one of his kidneys. she places it on a metal dish and grabbed a needle ready to stitch. she didn't stitch him up like he expected. the scientist removed his spleen as well causing Barry to scream as she did this more painfully and slowly so all he could fell was pain.

Barry's scream could be heard from the cells.

"what are they doing to him?" Iris asked worriedly.

"i don't know" Joe said honestly.

more screams could be heard from the torturous lab.

Iris tried to block them out. every scream that she hears, a part of her feels like dying.

Barry stopped screaming as she stopped. his spleen was placed on the dish along with his kidney.

"you want anything else while your at it?" he spat at them.

"we are one for now" she said to the man.

the blonde woman grabbed the needle and started to stitch him up. she wiped up most of the blood and put his top back on him. blood started to show through. he was unchained and Pushed to the door where they kept pushing him until he reached his cell. he was locked in once again.

"do you realise you have basically just killed me now?" Barry said to them.

"your not going to die... not yet anyway" the man replied.

"you have to stay alive in order to find out more" the woman said "that was hardly anything."

the scientists walked out and closed the door.


	4. Chapter 4

**A/N: Just as a warning this chapter involves more blood and a bit of gore. this is also a warning for further chapters in case of blood, gore and violence. You are warned.**

* * *

"Barry?" Iris asked.

"Yeah?" Barry replied.

"what did they do to you?" Iris aked.

everyone looked at Barry expecting him to say.

"And please answer" Iris said quickly.

"they removed some organs" Barry said.

"what organs?" Caitlin asked.

"A kidney and spleen" Barry replied.

"did they use something like a strong painkiller, disinfectant and something?" Caitlin asked worriedly.

"No, they just put me on the table, got a scalpel and started cutting" Barry replied.

"They stitched you right?" Caitlin asked.

"Yeah" Barry replied.

Caitlins cell was next to Barry's as well as Joe's is.

"can I see if its done properly?" she asked.

"Yeah" Barry replied.

he moved next to the bars and allowed Caitlin to have a look.

"it seems to have been done properly but quickly like it was rushed to make it more painful" Caitlin said as she examined the wound.

a gust of wind came through the door leaving a trail of red lightning behind before disappearing instantly. They knew what and who that was.

"How do you like it so far" The Reverse Flash said in a teasing way with a smile on his face.

"wonderful, I think I might come back again" Barry said sarcastically.

"two out of eight" Reverse Flash said referring to the metahumans (and alien).

more scientists came through the door.

"whos next?" one of the scientists said.

"we have alien skin, speedster organs. what do we need now" Reverse Flash said to himself "how about more organs? maybe this time we take it from the kid"

he scientists nodded and walked to Wally's cell, unlocking it, and dragging him to the next room.

"And while your doing that, I'll take some revenge on the scarlet speedster" Reverse Flash said looking at Barry.

he flashed over there and took Barry out, flashed over to the wall with the chains. he then tied him up to the wall with rope instead of the chains. he did it there so his friends and family can watch their precious speedster be beaten by his worst enemy.

"I hope your all going to watch this" He said.

he flashed out of the room and back again. he came in holding a big kitchen knife.

"this is going to be good" He said dragging the knife across Barry's arm drawing blood.

the knife raked over that arm over and over again. Barry tightened his jaw so he wouldn't scream, partly because of his friends sake and partly because he didn't want him to know how much It hurt him. the knife was dragged across his other arm making that bleed as well. the knife was slashed across his stomach slowly making it more painful. the knife was getting closer to his face, the blade making contact with his cheek. blood slowly dripping down his face. the blood from his arms, face and stomach made its way to the floor, making a puddle of blood. Reverse Flash grinned as he saw the cuts on Barry. He raised the knife to Barry's hands and cutting the rope letting Barry fall to the ground. Reverse Flash grabbed Barry by the top and dragged him on to a chair.

his hands were tied behind him. Reverse Flash walked behind Barry and reached for his hands. he grabbed on his fingers and started braking them until every finger was broken. Reverse Flash was going to do something more to him but decided to spread out his joy and leave the rest for the next days. He untied Barry and threw him into his cell and locked it again. He then ran out of the room closing the door behind him.

"I think he ruined my top" Barry said trying to laugh a bit.

"you get tortured and the first thing you do is joke?" Iris said.

"trying to stay on the bright side here" Barry replied.

"There is no bright side" Iris said back.

"well I'm not giving up" Barry stated.

"its not like Arrow is going to do anything, he left a couple of minutes before we were taken so he won't know" Joe said.

"He already knows" Barry replied.

they all look at Barry like he's insane.

"when we were glued to the wall, I saw Julian in the closet. he's probally phoned oliver by know" Barry said.

"since when does Julian know Oliver is the arrow?" Joe asked.

"since he saw Oliver in S.T.A.R labs as the Arrow" Barry replied.

Wally was in the same room that Barry was in: the white, clean lab. Wally had been strapped to the table and was cut on his arm. Wally expected it to be on his stomach to remove an organ b they didn't. he then thought it was only Reverse Flash trying to get everyone worried. the scientists only cut his arm a bit, it wasn't eve deep and they then didn't do anything, they just watched it and held a timer. they watched his arm for an hour and stopped the timer.

"it took one hour for the speedsters arm to heal from a minor cut" the scientist that cut him said to the other scientist on the computer.

"take him back to his cell" the computer scientist said.

"wait" Wally said.

the scientists stopped what they were doing and looked at Wally.

"what were you doing?" Wally asked.

"to see how long your regenerative powers worked" the first scientist said.

"why?" Wally asked.

"no more questions" the second scientist said.

the first scientist grabbed Wally and lead him to his cell.

"Wally" Joe said as he saw Wally being put back into his cell.

"what did they do to you, you were gone for over an hour?" Iris said concerned.

"they just cut my arm to see how long it would take to heal" Wally replied.

"so I guess were next" Jesse said.

"most likely" Jax said.

"What happened to you?" Wally asked Barry seeing the blood.

"The Reverse Flash decided to take personal vendetta against Mr Allen" Martin Stein said from his cell.

"It looks bad" Wally said.

"I'll heal" Barry replied "we just got to hold until Arrow finds us."

"what happens if he doesn't?" Jax asked.

"Felicity can hack into any camera and look for facial recognition to find us and she will know which way we are and where we are, then she'll tell Arrow and they'll come and find us" Barry replied.

"What happens if there isn't any cameras around?" Jax asked.

"then she can track us from this" Barry said as he reached into his pocket and grabbed his coms that are from his flash suit.

"How long have you had that?" Jax asked.

"Since the beginning but i've only just remembered" Barry replied.

"so you could have just told them where to find us?" Jax said.

"its not that simple. You need to be in S.T.A.R labs to hear it and its turned off at S.T.A.R labs so unless they go back to S.T.A.R labs and turn on the coms, they wont hear it" Cisco replied.

"But if they figure out that I've got it then they could locate us" Barry added.


	5. Chapter 5

Oliver, Felicity and Diggs arrive at S.T.A.R labs. Julian was already in there waiting for them.

"Julian, right?" Oliver asks.

"yeah" Julian replies.

"so what's happened to Barry and everyone?" Felicity asked.

"General Eiling and the Reverse Flash kidnapped them" Julian replied.

"so you called us to help find them?" Diggs asked.

"Yeah, I have no idea on how to track people and I thought you guys would" Julian said.

"We track them a lot on the computers, I mean I do that" Felicity said.

"have you told any one of this?" Oliver asked.

"Not this story. I went to the CCPD as Barry and Joe work for them, I told them that both of them were feeling sick and probably can't go back to work for a while" Julian replied.

"Good, Telling the CCPD would mean risking their identities and also risking both the CCPD's lives and everyone Eiling and Reverse Flash have kidnapped" Oliver said.

"I shall get to work" Felicity said walking to the computers.

she sat down and started typing. she started running the facial recognition scan of the whole city. That didn't work so she tried doing a Local scan of cities around. that also failed. she hacked into the satellite and did a world wide scan. Nothing, its like they vanished off the Earth.

"Hey. What's going on?" a voice said from the door way.

"Who are you?" Oliver asked.

"I'm Harrison wells but call me HR" HR said.

it took a moment to realise why they didn't recognise him.

"I'm sorry, I forgot" HR said as he took out a device from his pocket and pressed a button ( **A/N: the device he uses in season 3 so he can go out in public without being recognised as wells, but team flash sees him as wells. I hope you know what I'm on about- if not its on the episode with Shade in)**.

"What is that?" Diggs asked.

"its a device which lets me not look like Harrison wells. As Cisco and Caitlin told me, Dr. Wells is a murderer which would be arrested. so I decided I don't want to get arrested so I'm using this" HR explained.

"What?" Diggs said confused.

"I'm Harrison Wells from a different Earth" HR explained.

"That still doesn't make sense" Diggs said.

"No time to explain the logic of that, we have to find everyone" Felicity said from the computer.

"You guys didn't answer my question: What is going on?" Hr asked again.

They explained the situation to HR. Julian saw the Flash suit on its normal mannequin. Something didn't look quite right. He figured it out: The mannequin was facing a different direction to usual. Julian walks up to the suit and checks it to see why it was facing a different direction than normal. emblem in the middle was there, the left communicator was there BUT the right communicator wasn't there. Only one of Barry's coms were there.

"Hey guys?" Julian said getting their attention.

"Yes?" Oliver said.

"The suit is missing a communicator" Julian stated.

"Maybe B.A has got it?" HR said.

"yeah, If Barry has it then I can track it" Felicity said excitedly.

Felicity speed walks to the computer and turns it on. she does her hacking thing and try's to find a location. Nothing, No location.

"Maybe you need to turn the communicator on?" Diggs said.

Felicity activates the communicator.

"I knew that" Felicity said slowly.

She does her hacking again and ends up getting a signal through but no location.

"Barry?" Felicity said seeing if he could hear her.

* * *

 _"Barry?"_ A female voice- Felicity's voice- could be heard from Barry's pocket.

Barry grabbed the communicator out of his pocket. Everyone in the rom looked at Barry. Thank God, it was only Him and his Friends in the room.

"Felicity?" Barry said.

 _"Finally it worked"_ Felicity said _"Where are you?"_

"In a military Base somewhere" Barry replied.

Barry looked around the room for signs of exactly which one. One the walls was 1 painted in big, bold, white writing.

"Something tells me that we're in Base 1" Barry said.

 _"How do you know that?"_ Felicity asked.

"No time to explain" Barry replied


	6. Chapter 6

**A/N: sorry to the people who loved/liked this story. I kind of gave up on this. I didn't know how to finish this or where to go with this. sorry again for discontinuing it.**


End file.
